def test_parse_crab(self): f = data_stream('crab.nbrf') seqs = nbrf_io.read(f) self.assertEqual(seqs[0].alphabet, protein_alphabet) self.assertEqual(len(seqs), 9) self.assertEqual(seqs[2].name, "CRAB_CHICK") self.assertEqual(seqs[2].description, "ALPHA CRYSTALLIN B CHAIN (ALPHA(B)-CRYSTALLIN).") f.close()
def test_pir_file_from_clustal(self): f = data_stream('clustalw.pir') seqs = nbrf_io.read(f) self.assertEqual(len(seqs), 2) self.assertEqual( seqs[1].endswith( 'C-AATC-G-CAATG-G--CTTGAACCGGGTAAAAGTCGT-A----------------------------------------' '-----------------------------------------'), True) f.close()
def test_parse_cox2(self): f = data_stream('cox2.nbrf') seqs = nbrf_io.read(f) self.assertEqual(len(seqs), 5) self.assertEqual(len(seqs[1]), 210) self.assertEqual( str(seqs[0]), "MAFILSFWMIFLLDSVIVLLSFVCFVCVWICALLFSTVLLVSKLNNIYCTWDFTASKFIDVYWFTIGGMFSLG" "LLLRLCLLLYFGHLNFVSFDLCKVVGFQWYWVYFIFGETTIFSNLILESDYMIGDLRLLQCNHVLTLLSLVIY" "KLWLSAVDVIHSFAISSLGVKVENLVAVMK") self.assertEqual(seqs[0].alphabet, protein_alphabet) f.close()
def test_parse_protein(self): f = data_stream('protein.pir') seqs = nbrf_io.read(f) self.assertEqual(seqs[0].alphabet, protein_alphabet) self.assertEqual(len(seqs), 10) f.close()
def test_parse_examples(self): f = data_stream('rhod.pir') seqs = nbrf_io.read(f) self.assertEqual(seqs[0].alphabet, protein_alphabet) self.assertEqual(len(seqs), 3) f.close()
def test_parse_dna(self): f = data_stream('dna.pir') seqs = nbrf_io.read(f) self.assertEqual(seqs[0].alphabet, dna_alphabet) self.assertEqual(len(seqs), 10) f.close()